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Article ; Online: The 'Alu-ome' shapes the epigenetic environment of regulatory elements controlling cellular defense.

Costallat, Mickael / Batsché, Eric / Rachez, Christophe / Muchardt, Christian

2022 Volume 50, Issue 9, Page(s) 5095–5110

Abstract: Promoters and enhancers are sites of transcription initiation (TSSs) and carry specific histone modifications, including H3K4me1, H3K4me3, and H3K27ac. Yet, the principles governing the boundaries of such regulatory elements are still poorly ... ...

Abstract	Promoters and enhancers are sites of transcription initiation (TSSs) and carry specific histone modifications, including H3K4me1, H3K4me3, and H3K27ac. Yet, the principles governing the boundaries of such regulatory elements are still poorly characterized. Alu elements are good candidates for a boundary function, being highly abundant in gene-rich regions, while essentially excluded from regulatory elements. Here, we show that the interval ranging from TSS to first upstream Alu, accommodates all H3K4me3 and most H3K27ac marks, while excluding DNA methylation. Remarkably, the average length of these intervals greatly varies in-between tissues, being longer in stem- and shorter in immune-cells. The very shortest TSS-to-first-Alu intervals were observed at promoters active in T-cells, particularly at immune genes, where first-Alus were traversed by RNA polymerase II transcription, while accumulating H3K4me1 signal. Finally, DNA methylation at first-Alus was found to evolve with age, regressing from young to middle-aged, then recovering later in life. Thus, the first-Alus upstream of TSSs appear as dynamic boundaries marking the transition from DNA methylation to active histone modifications at regulatory elements, while also participating in the recording of immune gene transcriptional events by positioning H3K4me1-modified nucleosomes.
MeSH term(s)	Epigenesis, Genetic ; Epigenomics ; Histone Code ; Promoter Regions, Genetic ; Regulatory Sequences, Nucleic Acid
Language	English
Publishing date	2022-05-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkac346
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Article ; Online: Transcriptional activity of endogenous retroviruses in multiple sclerosis: a sign of deficient chromatin-mediated silencing.

Muchardt, Christian

Epigenomics

2015 Volume 7, Issue 8, Page(s) 1235–1237

MeSH term(s)	Chromatin/genetics ; Chromatin/metabolism ; Endogenous Retroviruses/genetics ; Gene Silencing ; Humans ; Multiple Sclerosis/etiology ; Multiple Sclerosis/metabolism ; Transcriptional Activation
Chemical Substances	Chromatin
Language	English
Publishing date	2015
Publishing country	England
Document type	Editorial
ISSN	1750-192X
ISSN (online)	1750-192X
DOI	10.2217/epi.15.81
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Article ; Online: A few thoughts about catalyzing transcription.

Muchardt, Christian

Epigenomics

2010 Volume 2, Issue 1, Page(s) 1–3

MeSH term(s)	Chromatin/metabolism ; Epigenesis, Genetic/genetics ; Epigenesis, Genetic/physiology ; Histone Acetyltransferases/metabolism ; Regulatory Elements, Transcriptional/physiology ; Transcription Factors/physiology ; Transcriptional Activation/genetics ; Transcriptional Activation/physiology
Chemical Substances	Chromatin ; Transcription Factors ; Histone Acetyltransferases (EC 2.3.1.48)
Language	English
Publishing date	2010-02
Publishing country	England
Document type	Editorial
ISSN	1750-192X
ISSN (online)	1750-192X
DOI	10.2217/epi.09.51
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Article: RB and c-Myc activate expression of the E-cadherin gene in epithelial cells through interaction with transcription factor AP-2.

Batsché, E / Muchardt, C / Behrens, J / Hurst, H C / Crémisi, C

Molecular and cellular biology

1998 Volume 18, Issue 7, Page(s) 3647–3658

Abstract: ... conversion associated with invasiveness and a down-regulation of c-Myc. Reexpression of RB or c-Myc ... c-Myc specifically activate transcription of the E-cadherin promoter in epithelial cells but not ... the oncoprotein binding domain and C-terminal domain of RB. In vivo physical interaction between RB and AP-2 was ...

Abstract	E-cadherin plays a pivotal role in the biogenesis of the first epithelium during development, and its down-regulation is associated with metastasis of carcinomas. We recently reported that inactivation of RB family proteins by simian virus 40 large T antigen (LT) in MDCK epithelial cells results in a mesenchymal conversion associated with invasiveness and a down-regulation of c-Myc. Reexpression of RB or c-Myc in such cells allows the reexpression of epithelial markers including E-cadherin. Here we show that both RB and c-Myc specifically activate transcription of the E-cadherin promoter in epithelial cells but not in NIH 3T3 mesenchymal cells. This transcriptional activity is mediated in both cases by the transcription factor AP-2. In vitro AP-2 and RB interaction involves the N-terminal domain of AP-2 and the oncoprotein binding domain and C-terminal domain of RB. In vivo physical interaction between RB and AP-2 was demonstrated in MDCK and HaCat cells. In LT-transformed MDCK cells, LT, RB, and AP-2 were all coimmunoprecipitated by each of the corresponding antibodies, and a mutation of the RB binding domain of the oncoprotein inhibited its binding to both RB and AP-2. Taken together, our results suggest that there is a tripartite complex between LT, RB, and AP-2 and that the physical and functional interactions between LT and AP-2 are mediated by RB. Moreover, they define RB and c-Myc as coactivators of AP-2 in epithelial cells and shed new light on the significance of the LT-RB complex, linking it to the dedifferentiation processes occurring during tumor progression. These data confirm the important role for RB and c-Myc in the maintenance of the epithelial phenotype and reveal a novel mechanism of gene activation by c-Myc.
MeSH term(s)	3T3 Cells ; Animals ; Antigens, Polyomavirus Transforming/genetics ; Cadherins/genetics ; Cell Line ; Cell Line, Transformed ; DNA-Binding Proteins/metabolism ; Dogs ; Epithelial Cells/metabolism ; Gene Expression Regulation ; Genes, myc ; Humans ; Mice ; Promoter Regions, Genetic ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Retinoblastoma Protein/genetics ; Retinoblastoma Protein/metabolism ; Transcription Factor AP-2 ; Transcription Factors/metabolism ; Transcriptional Activation ; Tumor Cells, Cultured
Chemical Substances	Antigens, Polyomavirus Transforming ; Cadherins ; DNA-Binding Proteins ; Recombinant Fusion Proteins ; Retinoblastoma Protein ; Transcription Factor AP-2 ; Transcription Factors
Language	English
Publishing date	1998-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	779397-2
ISSN	1098-5549 ; 0270-7306
ISSN (online)	1098-5549
ISSN	0270-7306
DOI	10.1128/MCB.18.7.3647
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Article ; Online: HP1γ binding pre-mRNA intronic repeats modulates RNA splicing decisions.

Rachez, Christophe / Legendre, Rachel / Costallat, Mickaël / Varet, Hugo / Yi, Jia / Kornobis, Etienne / Muchardt, Christian

EMBO reports

2021 Volume 22, Issue 9, Page(s) e52320

Abstract: HP1 proteins are best known as markers of heterochromatin and gene silencing. Yet, they are also RNA-binding proteins and the HP1γ/CBX3 family member is present on transcribed genes together with RNA polymerase II, where it regulates co-transcriptional ... ...

Abstract	HP1 proteins are best known as markers of heterochromatin and gene silencing. Yet, they are also RNA-binding proteins and the HP1γ/CBX3 family member is present on transcribed genes together with RNA polymerase II, where it regulates co-transcriptional processes such as alternative splicing. To gain insight in the role of the RNA-binding activity of HP1γ in transcriptionally active chromatin, we have captured and analysed RNAs associated with this protein. We find that HP1γ is specifically targeted to hexameric RNA motifs and coincidentally transposable elements of the SINE family. As these elements are abundant in introns, while essentially absent from exons, the HP1γ RNA association tethers unspliced pre-mRNA to chromatin via the intronic regions and limits the usage of intronic cryptic splice sites. Thus, our data unveil novel determinants in the relationship between chromatin and co-transcriptional splicing.
MeSH term(s)	Alternative Splicing/genetics ; Introns/genetics ; RNA Precursors/genetics ; RNA Precursors/metabolism ; RNA Splicing/genetics ; RNA-Binding Proteins
Chemical Substances	RNA Precursors ; RNA-Binding Proteins
Language	English
Publishing date	2021-07-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.15252/embr.202052320
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Zs.A 5433: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: The Influenza Virus RNA-Polymerase and the Host RNA-Polymerase II: RPB4 Is Targeted by a PB2 Domain That Is Involved in Viral Transcription.

Morel, Jessica / Sedano, Laura / Lejal, Nathalie / Da Costa, Bruno / Batsché, Eric / Muchardt, Christian / Delmas, Bernard

Viruses

2022 Volume 14, Issue 3

Abstract: ... to the flexible C-terminal domain (CTD) of the RPB1 subunit of RNA-polymerase II (Pol II). To better understand ... by a co-immunoprecipitation assay and was found to occur with the homologous domains of influenza B and C FluPols. The N-half ... positions between influenza A, B, and C FluPols in the N-third domain of PB2 exhibited strong ...

Abstract	Influenza virus transcription is catalyzed by the viral RNA-polymerase (FluPol) through a cap-snatching activity. The snatching of the cap of cellular mRNA by FluPol is preceded by its binding to the flexible C-terminal domain (CTD) of the RPB1 subunit of RNA-polymerase II (Pol II). To better understand how FluPol brings the 3'-end of the genomic RNAs in close proximity to the host-derived primer, we hypothesized that FluPol may recognize additional Pol II subunits/domains to ensure cap-snatching. Using binary complementation assays between the Pol II and influenza A FluPol subunits and their structural domains, we revealed an interaction between the N-third domain of PB2 and RPB4. This interaction was confirmed by a co-immunoprecipitation assay and was found to occur with the homologous domains of influenza B and C FluPols. The N-half domain of RPB4 was found to be critical in this interaction. Punctual mutants generated at conserved positions between influenza A, B, and C FluPols in the N-third domain of PB2 exhibited strong transcriptional activity defects. These results suggest that FluPol interacts with several domains of Pol II (the CTD to bind Pol II), initiating host transcription and a second transcription on RPB4 to locate FluPol at the proximity of the 5'-end of nascent host mRNA.
MeSH term(s)	Humans ; Influenza, Human ; Orthomyxoviridae/genetics ; RNA Polymerase II/metabolism ; RNA, Messenger/genetics ; RNA, Viral/genetics ; RNA, Viral/metabolism ; RNA-Dependent RNA Polymerase/genetics ; Viral Transcription ; Virus Replication
Chemical Substances	RNA, Messenger ; RNA, Viral ; RNA Polymerase II (EC 2.7.7.-) ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
Language	English
Publishing date	2022-03-03
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14030518
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Article ; Online: Expression of endogenous retroviruses reflects increased usage of atypical enhancers in T cells.

Azébi, Saliha / Batsché, Eric / Michel, Frédérique / Kornobis, Etienne / Muchardt, Christian

The EMBO journal

2019 Volume 38, Issue 12

Abstract: Several autoimmune diseases including multiple sclerosis (MS) cause increased transcription of endogenous retroviruses (HERVs) normally repressed by heterochromatin. In parallel, HERV-derived sequences were reported to drive gene expression. Here, we ... ...

Abstract	Several autoimmune diseases including multiple sclerosis (MS) cause increased transcription of endogenous retroviruses (HERVs) normally repressed by heterochromatin. In parallel, HERV-derived sequences were reported to drive gene expression. Here, we have examined a possible link between promoter and enhancer divergent transcription and the production of HERV transcripts. We find that HERV-derived sequences are in general counter-selected at regulatory regions, a counter-selection that is strongest in brain tissues while very moderate in stem cells. By exposing T cells to the pesticide dieldrin, we further found that a series of HERV-driven enhancers otherwise active only at stem cell stages can be reactivated by stress. This in part relies on peptidylarginine deiminase activity, possibly participating in the reawakening of silenced enhancers. Likewise, usage of HERV-driven enhancers was increased in myelin-reactive T cells from patients with MS, correlating with activation of nearby genes at several sites. Altogether, we propose that HERV-driven enhancers constitute a reservoir of auxiliary enhancers transiently induced by stress while chronically active in diseases like MS.
MeSH term(s)	Adult ; Case-Control Studies ; Cells, Cultured ; Endogenous Retroviruses/genetics ; Female ; Gene Expression Regulation, Viral/physiology ; Humans ; Jurkat Cells ; Male ; Middle Aged ; Multiple Sclerosis/genetics ; Multiple Sclerosis/immunology ; Multiple Sclerosis/metabolism ; Multiple Sclerosis/virology ; Regulatory Sequences, Nucleic Acid/genetics ; T-Lymphocytes/metabolism ; T-Lymphocytes/pathology
Language	English
Publishing date	2019-05-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	586044-1
ISSN	1460-2075 ; 0261-4189
ISSN (online)	1460-2075
ISSN	0261-4189
DOI	10.15252/embj.2018101107
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Zs.A 1808: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 100: Show issues

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Article: Regulation of human immunodeficiency virus enhancer function by PRDII-BF1 and c-rel gene products.

Muchardt, C / Seeler, J S / Nirula, A / Shurland, D L / Gaynor, R B

Journal of virology

1992 Volume 66, Issue 1, Page(s) 244–250

Abstract: ... have been cloned. We characterized the binding of proteins encoded by the human c-rel and PRDII-BF1 ... genes to HIV NF-kappa B motifs and related enhancer elements. Both the human c-rel protein and two ... of the PRDII-BF1 gene or the c-rel gene to the DNA binding region of the yeast transcription factor GAL4. GAL4 ...

Abstract	The human immunodeficiency virus (HIV) enhancer element is important in the regulation of HIV gene expression. A number of cellular proteins have been demonstrated to bind to the NF-kappa B motifs in this element. The genes encoding several of these proteins, including members of the rel family and PRDII-BF1, have been cloned. We characterized the binding of proteins encoded by the human c-rel and PRDII-BF1 genes to HIV NF-kappa B motifs and related enhancer elements. Both the human c-rel protein and two proteins derived from the PRDII-BF1 gene by alternative splicing bound specifically to the HIV NF-kappa B motif and related enhancer elements found in the immunoglobulin kappa, class I major histocompatibility complex, and interleukin-2 receptor genes. To determine the role of these factors in regulating HIV gene expression, we fused the cDNAs encoding either of the two proteins derived by alternative splicing of the PRDII-BF1 gene or the c-rel gene to the DNA binding region of the yeast transcription factor GAL4. GAL4 binding sites were inserted in place of the native HIV enhancer sequences in an HIV long terminal repeat chloramphenicol acetyltransferase construct. Cotransfection of these constructs revealed that c-rel was a strong activator of basal HIV gene expression but did not result in synergistic effects in the presence of tat. PRDII-BF1-derived cDNAs did not result in stimulation of either basal or tat-induced activated gene expression. These results indicate that multiple enhancer binding proteins may potentially regulate HIV in both a positive and negative manner.
MeSH term(s)	Base Sequence ; Blotting, Northern ; Blotting, Southern ; Cloning, Molecular ; DNA, Viral/metabolism ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Gene Expression Regulation, Viral ; HIV/genetics ; HIV Enhancer ; Humans ; Molecular Sequence Data ; NF-kappa B/metabolism ; Protein Binding ; Protein Biosynthesis ; Proto-Oncogene Proteins/genetics ; Proto-Oncogene Proteins/metabolism ; Proto-Oncogene Proteins c-rel ; RNA Splicing ; RNA, Viral/metabolism ; Transcription Factors
Chemical Substances	DNA, Viral ; DNA-Binding Proteins ; HIVEP1 protein, human ; NF-kappa B ; Proto-Oncogene Proteins ; Proto-Oncogene Proteins c-rel ; RNA, Viral ; Transcription Factors
Language	English
Publishing date	1992-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.66.1.244-250.1992
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Zs.A 609: Show issues

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Article ; Online: Reduced RNA turnover as a driver of cellular senescence.

Mullani, Nowsheen / Porozhan, Yevheniia / Mangelinck, Adèle / Rachez, Christophe / Costallat, Mickael / Batsché, Eric / Goodhardt, Michele / Cenci, Giovanni / Mann, Carl / Muchardt, Christian

Life science alliance

2021 Volume 4, Issue 3

Abstract: Accumulation of senescent cells is an important contributor to chronic inflammation upon aging. The inflammatory phenotype of senescent cells was previously shown to be driven by cytoplasmic DNA. Here, we propose that cytoplasmic double-stranded RNA has ... ...

Abstract	Accumulation of senescent cells is an important contributor to chronic inflammation upon aging. The inflammatory phenotype of senescent cells was previously shown to be driven by cytoplasmic DNA. Here, we propose that cytoplasmic double-stranded RNA has a similar effect. We find that several cell types driven into senescence by different routes share an accumulation of long promoter RNAs and 3' gene extensions rich in retrotransposon sequences. Accordingly, these cells display increased expression of genes involved in response to double stranded RNA of viral origin downstream of the interferon pathway. The RNA accumulation is associated with evidence of reduced RNA turnover, including in some cases, reduced expression of RNA exosome subunits. Reciprocally, depletion of RNA exosome subunit EXOSC3 accelerated expression of multiple senescence markers. A senescence-like RNA accumulation was also observed in cells exposed to oxidative stress, an important trigger of cellular senescence. Altogether, we propose that in a subset of senescent cells, repeat-containing transcripts stabilized by oxidative stress or reduced RNA exosome activity participate in driving and maintaining the permanent inflammatory state characterizing cellular senescence.
MeSH term(s)	Cell Line ; Cellular Senescence/genetics ; DNA Damage ; Humans ; Inflammation/metabolism ; Oxidative Stress/genetics ; Phenotype ; RNA/genetics ; RNA/metabolism ; RNA Stability/genetics ; RNA, Double-Stranded/adverse effects ; RNA, Double-Stranded/genetics ; Retroelements/genetics
Chemical Substances	RNA, Double-Stranded ; Retroelements ; RNA (63231-63-0)
Language	English
Publishing date	2021-01-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2575-1077
ISSN (online)	2575-1077
DOI	10.26508/lsa.202000809
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Article ; Online: CD44 alternative splicing senses intragenic DNA methylation in tumors via direct and indirect mechanisms.

Batsché, Eric / Yi, Jia / Mauger, Oriane / Kornobis, Etienne / Hopkins, Benjamin / Hanmer-Lloyd, Charlotte / Muchardt, Christian

Nucleic acids research

2021 Volume 49, Issue 11, Page(s) 6213–6237

Abstract: DNA methylation (meDNA) is a modulator of alternative splicing, and splicing perturbations are involved in tumorigenesis nearly as frequently as DNA mutations. However, the impact of meDNA on tumorigenesis via splicing-mediated mechanisms has not been ... ...

Abstract	DNA methylation (meDNA) is a modulator of alternative splicing, and splicing perturbations are involved in tumorigenesis nearly as frequently as DNA mutations. However, the impact of meDNA on tumorigenesis via splicing-mediated mechanisms has not been thoroughly explored. Here, we found that HCT116 colon carcinoma cells inactivated for the DNA methylases DNMT1/3b undergo a partial epithelial to mesenchymal transition associated with increased CD44 variant exon skipping. These skipping events are directly mediated by the loss of intragenic meDNA and the chromatin factors MBD1/2/3 and HP1γ and are also linked to phosphorylation changes in elongating RNA polymerase II. The role of meDNA in alternative splicing was confirmed by using the dCas9/DNMT3b tool. We further tested whether the meDNA level could have predictive value in the MCF10A model for breast cancer progression and in patients with acute lymphoblastic leukemia (B ALL). We found that a small number of differentially spliced genes, mostly involved in splicing and signal transduction, are correlated with the local modulation of meDNA. Our observations suggest that, although DNA methylation has multiple avenues to affect alternative splicing, its indirect effect may also be mediated through alternative splicing isoforms of these meDNA sensors.
MeSH term(s)	Alternative Splicing ; Breast Neoplasms/genetics ; Breast Neoplasms/metabolism ; Carcinogenesis/genetics ; Cell Line, Tumor ; Chromobox Protein Homolog 5 ; Chromosomal Proteins, Non-Histone/metabolism ; DNA (Cytosine-5-)-Methyltransferase 1/genetics ; DNA (Cytosine-5-)-Methyltransferases/genetics ; DNA Methylation ; DNA-Binding Proteins/metabolism ; Epithelial-Mesenchymal Transition ; Exons ; Female ; Gene Expression Regulation, Neoplastic ; HeLa Cells ; Histone Code ; Humans ; Hyaluronan Receptors/genetics ; Hyaluronan Receptors/metabolism ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/metabolism ; RNA Polymerase II/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic ; DNA Methyltransferase 3B
Chemical Substances	CD44 protein, human ; Chromosomal Proteins, Non-Histone ; DNA-Binding Proteins ; Hyaluronan Receptors ; MBD1 protein, human ; Transcription Factors ; Chromobox Protein Homolog 5 (107283-02-3) ; DNA (Cytosine-5-)-Methyltransferase 1 (EC 2.1.1.37) ; DNA (Cytosine-5-)-Methyltransferases (EC 2.1.1.37) ; DNMT1 protein, human (EC 2.1.1.37) ; RNA Polymerase II (EC 2.7.7.-)
Language	English
Publishing date	2021-06-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkab437
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